LAST UPDATE AT
[1] "Thu Nov 28 22:01:06 2019"
This html file belongs to the Manuscript:
“Dissecting intratumor heterogeneity of nodal B cell lymphoma on the transcriptional, genetic, and drug response level” Roider et al.
doi: …
It summarizes differentially expressed genes between different B cell subpopulations in malignant lymphoma samples. It enables the readers to browse differentially expressed genes for each B cell subpopulation interactively. Only genes with a minimal log fold change of 0.25 and an adjusted p value < 0.05 are shown.
Sample abbreviations:
DLBCL: Diffuse large B cell lymphoma
tFL: Transformed follicular lymphoma
FL: Follicular lymphopma
rLN: Reactive lymph node (non-malignant controls)
get.data extracts most important meta data and feature data, and puts them into a data frame.
get.data <- function(Sobj, genes) {
# Extract Meta data
df.meta <- data.frame(Cluster = Sobj@ident, Sobj@meta.data)
# Extract tSNE coordinates if available
if(!is.null(Sobj@dr$tsne))
{
df.meta <- cbind(df.meta, Sobj@dr$tsne@cell.embeddings)
}
# Extract umap coordinates if available
if(!is.null(Sobj@dr$umap))
{
df.meta <- cbind(df.meta, Sobj@dr$umap@cell.embeddings)
}
# Extract gene expression data for expressed genes
genes.red <- rownames(Sobj@data)[rownames(Sobj@data) %in% genes]
dftotal <- cbind(df.meta, FetchData(Sobj, genes.red))
return(dftotal)
}plot.TSNE creates tSNE plots from Seurat objects in ggplot style.
get.data(TotalMerge_B, "") %>%
ggplot(aes(x=UMAP1, y=UMAP2, color=Cluster))+geom_point(size=0.75)+
guides(color = guide_legend(override.aes = list(size = 3)))+
theme_bw() R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.1
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] DT_0.9 dplyr_0.8.3 Seurat_2.3.4 Matrix_1.2-17
[5] cowplot_1.0.0 ggplot2_3.2.1 knitr_1.25 BiocStyle_2.12.0
loaded via a namespace (and not attached):
[1] Rtsne_0.15 colorspace_1.4-1 class_7.3-15
[4] modeltools_0.2-22 ggridges_0.5.1 mclust_5.4.5
[7] htmlTable_1.13.2 base64enc_0.1-3 rstudioapi_0.10
[10] proxy_0.4-23 npsurv_0.4-0 flexmix_2.3-15
[13] bit64_0.9-7 codetools_0.2-16 splines_3.6.1
[16] R.methodsS3_1.7.1 lsei_1.2-0 robustbase_0.93-5
[19] zeallot_0.1.0 jsonlite_1.6 Formula_1.2-3
[22] ica_1.0-2 cluster_2.1.0 kernlab_0.9-27
[25] png_0.1-7 R.oo_1.23.0 shiny_1.4.0
[28] BiocManager_1.30.9 compiler_3.6.1 httr_1.4.1
[31] backports_1.1.5 fastmap_1.0.1 assertthat_0.2.1
[34] lazyeval_0.2.2 later_1.0.0 lars_1.2
[37] acepack_1.4.1 htmltools_0.4.0 tools_3.6.1
[40] igraph_1.2.4.1 gtable_0.3.0 glue_1.3.1
[43] RANN_2.6.1 reshape2_1.4.3 Rcpp_1.0.2
[46] vctrs_0.2.0 gdata_2.18.0 ape_5.3
[49] nlme_3.1-141 crosstalk_1.0.0 iterators_1.0.12
[52] fpc_2.2-3 gbRd_0.4-11 lmtest_0.9-37
[55] xfun_0.10 stringr_1.4.0 mime_0.7
[58] lifecycle_0.1.0 irlba_2.3.3 gtools_3.8.1
[61] DEoptimR_1.0-8 MASS_7.3-51.4 zoo_1.8-6
[64] scales_1.0.0 promises_1.1.0 doSNOW_1.0.18
[67] parallel_3.6.1 RColorBrewer_1.1-2 yaml_2.2.0
[70] reticulate_1.13 pbapply_1.4-2 gridExtra_2.3
[73] rpart_4.1-15 segmented_1.0-0 latticeExtra_0.6-28
[76] stringi_1.4.3 foreach_1.4.7 checkmate_1.9.4
[79] caTools_1.17.1.2 bibtex_0.4.2 Rdpack_0.11-0
[82] SDMTools_1.1-221.1 rlang_0.4.1 pkgconfig_2.0.3
[85] dtw_1.21-3 prabclus_2.3-1 bitops_1.0-6
[88] evaluate_0.14 lattice_0.20-38 ROCR_1.0-7
[91] purrr_0.3.3 labeling_0.3 htmlwidgets_1.5.1
[94] bit_1.1-14 tidyselect_0.2.5 plyr_1.8.4
[97] magrittr_1.5 bookdown_0.14 R6_2.4.0
[100] snow_0.4-3 gplots_3.0.1.1 Hmisc_4.2-0
[103] pillar_1.4.2 foreign_0.8-72 withr_2.1.2
[106] fitdistrplus_1.0-14 mixtools_1.1.0 survival_2.44-1.1
[109] nnet_7.3-12 tsne_0.1-3 tibble_2.1.3
[112] crayon_1.3.4 hdf5r_1.3.0 KernSmooth_2.23-16
[115] rmarkdown_1.16 grid_3.6.1 data.table_1.12.6
[118] metap_1.1 digest_0.6.22 diptest_0.75-7
[121] xtable_1.8-4 httpuv_1.5.2 tidyr_1.0.0
[124] R.utils_2.9.0 stats4_3.6.1 munsell_0.5.0